Eilam O., Zarecki R., Oberhardt M., Ursell L.K, Kupiec M., Knight R., Gophna U., Ruppin E..
2014. Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations. mBio. 5(4):e01526-14-e01526-14. |
Stempler S, Yizhak K, Ruppin E.
2014. Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease. PLoS ONE. 9(8):e105383. |
Timp W, Bravo HCorrada, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.
2014. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61. |
Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Segal EShtifman, Freilich S, Henry CS, Gophna U, Ruppin E.
2014. Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372. |
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.
2014. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.. Bioinformatics. 30(10):1363-9. |
Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al..
2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767. |
Yizhak K, Gaude E, Le Dévédec S, Waldman YY, Stein GY, van de Water B, Frezza C, Ruppin E.
2014. Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.. Elife. 3 |
Jerby-Arnon L, Pfetzer N, Waldman YY, McGarry L, James D, Shanks E, Seashore-Ludlow B, Weinstock A, Geiger T, Clemons PA et al..
2014. Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.. Cell. 158(5):1199-209. |
Khan Z, Wang Y-C, Wieschaus EF, Kaschube M.
2014. Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.. Development. 141(14):2895-900. |
Parker HS, Bravo HCorrada, Leek JT.
2014. Removing batch effects for prediction problems with frozen surrogate variable analysis.. PeerJ. 2:e561. |
Paulson JN, Bravo éctorCorrada, Pop M.
2014. Reply to: "A fair comparison". Nature Methods. 11(4):359-360. |
Akula N., Barb J., Jiang X., Wendland J.R, Choi K.H, Sen S.K, Hou L., Chen D.TW, Laje G., Johnson K. et al..
2014. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Molecular psychiatry. |
Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, Hou L, Chen DTW, Laje G, Johnson K et al..
2014. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.. Mol Psychiatry. 19(11):1179-85. |
Patro R, Mount SM, Kingsford C.
2014. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.. Nat Biotechnol. 32(5):462-4. |
Molden RC, Goya J, Khan Z, Garcia BA.
2014. Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination.. Mol Cell Proteomics. 13(4):1106-18. |
Baeza J, Dowell JA, Smallegan MJ, Fan J, Amador-Noguez D, Khan Z, Denu JM.
2014. Stoichiometry of site-specific lysine acetylation in an entire proteome.. J Biol Chem. 289(31):21326-38. |
Treangen T, Ondov BD, Koren S, Phillippy AM.
2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome biology. 15:524. |
Nguyen N-phuong, Mirarab S, Liu B, Pop M, Warnow T.
2014. TIPP:Taxonomic Identification and Phylogenetic Profiling. BioinformaticsBioinformatics. |